Hiroshima Ginkgo Trees

After discussing the ginkgo trees in class that survived the blasts, I decided to look for more information about the specific trees which were known to survive the atomic blasts. The closest tree to the blast was about 1.1km away from the blast and only survived by its roots which later sprang new buds (the entirety of the tree was otherwise blown away), and is found in front of a temple now. The remaining 6 trees remained partially if not fully intact due to their further distance from the blast and often buildings blocking them from the full blow. Culturally, these trees are now revered for their resilience and seen as symbols of hope and remembrance of the Hiroshima atrocity. Only one of the trees has been moved from its original location, with the rest being left exactly where it was during the bombing.
For more information and pictures of these trees check this link:
https://www.nytimes.com/2017/08/04/opinion/the-whispering-leaves-of-the-hiroshima-ginkgo-trees.html

REEF Recruitment for Spring 2019

Hey everyone, like I mentioned in class, the REEF is hiring for next quarter. If you think aquatic bio is something you might be interested in, it's definitely a great opportunity. I have linked the flyer that has information on when, where, and how to apply below.

Text me if you have any questions, (805) 215-2821

-Shey

REEF Spring 2019 Flyer

Link to Article About Split-Sex Animals

Given our recent discussions on biological sex or lack thereof in organisms, I found this recent New York Times article on gynandromorphs super interesting! The article discusses how organisms which show mosaic sex characteristics can help researchers explore sex-linked disease vulnerability. 

Here's the link:
https://www.nytimes.com/2019/02/25/science/split-sex-gynandromorph.html

McShea & Brandon's BIOLOGY’S FIRST LAW – controversial, but worth a read

To anyone searching for a cool theoretical biology/evolutionary mechanisms book, Biology’s First Law by Daniel W. McShea and Robert N. Brandon is a pretty radical read! While its arguments are too complex to summarize in one blog post, its overarching argument proposes genetic drift as the first Zero-Force Evolutionary Law (ZEFL) of biology:

“ZFEL (general formulation): In any evolutionary system in which there is variation and heredity, there is a tendency for diversity and complexity** to increase, one that is always present but may be opposed or augmented by natural selection, other forces, or constraints acting on diversity or complexity” (3).

“ZFEL (special formulation): In any evolutionary system in which there is variation and heredity, in the absence of natural selection, other forces, and constraints acting on diversity or complexity, diversity and complexity will increase on average” (4).

There are some problematic aspects to this argument, however. It’s unclear how much value it holds as a null hypothesis, and it conflicts with the traditional view of drift as a constraint on variation. In addition, a 2012 review, “Puzzles for ZFEL: McShea and Brandon’s zero force evolutionary law,” by Barret et. al, rebutes McShea and Brandon, deeming the special formulation of ZFEL impossible as if it holds true that mutations indicate the presence of a force, and the absence of mutations indicate a constraint of the force, then a force or a constraint must always be present (2012). ZFEL also butts heads with Hardy Weinberg equilibrium, which McShea and Brandon regard as “problematic as a zero-force law because it mixes genuine evolutionary forces … with a non-force, namely drift” (McShea, Brandon 100). But despite the dissent over ZEFL as a viable biological law, I still considered Biology’s First Law a valuable read. ZEFL is elegant, intuitive, and holds a potentially formative perspective on what we consider the “norm” in evolutionary history. I also found its contrast with inertia (the zero-force law of physics) intriguing.

Browsing the literature available about this hypothesis gave me an interesting glimpse into the philosophy of science and how theoretical disputes play out in the academic world. If any of you guys have also happened to have read this book, or have put it on your reading list, let me know what you think!

**defined as the number of part types” or “degree of differentiation among parts” to avoid the anthropocentric connotations of colloquial complexity.

Sloth Fur Could Hold the Cure to Human Diseases

 Sloths are among the few arboreal mammals; ecosystems unto themselves, their ovular outer hairs play host to algae, arthropods, and fungi, some species of which are endemic to sloth fur. The sloth’s relationships with their inhabitants range from commensalism to mutualism. Pauli et al. describe these relationships in their 2014 paper “A Syndrome of Mutualism Reinforces the Lifestyle of a Sloth.” The herbivorous sloths derive nutrition from their algal communities, with three-toed sloths hosting more algae and moths than their two-toed counterparts. 

            In addition to providing nutrients to the slow-moving mammals, the sloth-bound ecosystem may provide immense anthropogenic benefits. In their 2014 paper “Sloth Hair as a Novel Source of Fungi with Potent Anti-Parasitic, Anti-Cancer and Anti-Bacterial Bioactivity,” Higginbotham et al. investigate the possible medical benefits of these communities. As medicine begins to exhaust its investigation of soil-bound fungi in the search for new cures and discoveries, the sloth provides a litany of new fungal species. The researchers found 84 different fungi strains after culturing sloth hair. Of these, species were found that were active against malaria, Chagas disease, and a line of human breast cancer cells. Twenty out of fifty fungal extracts tested had antibiotic properties. The authors allude to further potential discoveries that could be made possible with more diverse and advanced testing. 

 

Sources: 

Higginbotham, S., Wong, W. R., Linington, R. G., Spadafora, C., Iturrado, L., & Arnold, A. E. (2014). Sloth Hair as a Novel Source of Fungi with Potent Anti-Parasitic, Anti-Cancer and Anti-Bacterial Bioactivity. PLoS ONE,9(1). doi:10.1371/annotation/10c47668-8c49-48d2-ba65-60420af463b6

 

Pauli, J. N., Mendoza, J. E., Steffan, S. A., Carey, C. C., Weimer, P. J., & Peery, M. Z. (2014). A syndrome of mutualism reinforces the lifestyle of a sloth. Proceedings of the Royal Society B: Biological Sciences, 281(1778), 20133006-20133006. doi:10.1098/rspb.2013.3006

 

Photo:

MEHLFÜHRER, C. (n.d.). The three-toed sloth Bradypus variegatus has the lowest field metabolic rate ever recorded, according to a new study.[Photograph]. Wikimedia Commons.

 

Darwinian Evolution of the Plants and Animals in the Radioactive Zones of Chernobyl and Fukushima (Video)

This is a video I found online while researching the ability of plants and animals to resist high levels of radioactivity, which was mentioned briefly in class. The New York Times reported on the efforts of Dr. Timothy Mousseau and the University of South Carolina efforts to investigate what has allowed for the regeneration of plant and animal populations in Chernobyl and Fukushima following some of the largest nuclear catastrophes of our modern era. Here is a link to the video: https://www.youtube.com/watch?v=TG-nwQBBfmc&t=14s. I highly recommend it to see some spectacular visuals that truly convey the incredible evidence of evolution in these plants and animals to be able to not only survive, but thrive in these areas. (Also, some excellent snarky YouTube comments :)). There are plenty of other documentaries on these adaptions to radiation on YouTube if you are interested, however, I thought this was concise and informative. If you are interested to read more about the project and Dr. Mousseau here is a link to the website that has some more information about the people involved and some publications associated with the project:
http://cricket.biol.sc.edu/chernobyl/Chernobyl_Research_Initiative/Introduction.html
With the abundance of money being poured into nuclear energy, this research may prove to be very informative...


-Ethan Subel

Treatment of Clostridium dificile and Related Intestinal Disorders by Fecal Microbiota Transplantation (FMT)

           Within our bodies, there exists a complex system of billions of beneficial microorganisms that is integral to our vitality. Whether it be on our skin or in our intestinal linings, these bacteria perform vital functions that assist in the maintenance of our health. These bacteria are affected by environmental factors, age, genetics, etc., and this is concerning due to the rise in obesity and associated metabolic conditions. These conditions can severely harm ones health and quality of life, and there is controversy surrounding the treatment. Since most of these are caused by deleterious bacteria, aggressive antibiotic treatments have been used to wipe out these pathogens. However, not only do these eliminate the mutualistic bacteria due to the lack of specificity in antibiotics, they also can cause immunity to develop in the harmful strain. This makes further development in antibiotics increasingly difficult, which has lead to research into an alternative form of treatment known as Fecal Microbiota Transplantation.

              Fecal Microbiota Transplantation (FMT) is the transplantation of gut flora between individuals by means of tubes through the anus or mouth to transport the sample to the desired location. This causes direct implantation of bacteria that will cause them to outcompete the negative bacteria in order to alleviate patients of the disease. It was approved by the FDA in the case of Clostridium dificile (C. dificile) infection due to the ineffectiveness of antibiotics. C. dificile is a bacteria that infects the colon and causes severe stomach difficulties. With respect to the efficiency in treatment, FMT proved to be upwards of 90% effective in remediating the symptoms of C. dificile (Marotz, 2016). The efficacy of FMT in C. dificile has led to subsequent research into “superdonors”. These individuals provide a better therapeutic affect and are thought to be either people who live in the same conditions as the patient or contain a keystone bacterial species. Although it is not explicitly clear yet, further research aims at finding what makes these people “superdonors” by testing samples with high concentrations of different strains of gut flora. Although there are many positive aspects to this type of treatment, there are several drawbacks. Besides the obvious social stigma and concerns, many test subjects are very ill so it is very hard to tell whether the FMT brought about even more illness due to the transfer of bacteria. Also, there is extreme varying in success, and the difference between a 90+% and 20% effectiveness can be the difference between the technique being approved for further treatment or not. Finally, there may be other unintended systemic affects, however, these may be outweighed by the benefits of the FMT procedure.

-Ethan Subel

LINK TO PAPER: 

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5045147/

Marotz, Clarisse, Zarrinpar, Amir. 2016. “Treating Obesity and                            Metabolic Syndrome with Fecal Microbiota Transplantation”.                        Yale Journal of Biology and Medicine, 89: 383-388.

Huge Sunfish!

I decided to go for a morning stroll on the beach and came across this huge sunfish! Sea gulls were already making their way to contribute to the circle of life, so I thought I would snap a picture before the fish was completely eaten. You never know what's going to wash up on shore in Santa Barbara!

- Emily Hascall

Neutralism vs. Selectionism

In researching MHC compatibility, which we talked about in class and which Lilly wrote a great post about, I stumbled upon a different topic and fell into a Google rabbit hole. In S. B. Piertney and M. K. Oliver’s 2006 paper “The Evolutionary Ecology of the Major Histocompatibility Complex,” the authors allude to “the neutralism vs. selectionism debate.” While trying to understand what this debate entails, I found a 2005 article by Masatoshi Nei, “Selectionism and Neutralism in Molecular Evolution.” 

Nei has been in the field of evolutionary biology for over 40 years, and the paper offers a history of the changing ideas surrounding neutralism vs. selectionism in the past century. Those on the selectionism side (whom the author calls “Neo-Darwinists”) argue that genetic change occurs almost entirely through positive and negative natural selection, and can occur even without new mutation in a population. This side of the debate was strongest in the 1950s and ’60s, but eventually new technology allowed the pendulum to swing back toward the ideas of neutralism. 

Neutralism was conceived by Thomas Morgan, who believed neutral mutations occurring was more important for evolution than natural selection was. He argued that natural selection selects for positive mutations and eliminates deleterious ones and that most mutations are neutral and become fixed due to genetic drift. Nei points out that according to this theory, “any number of substitutions is possible as long as the substitution rate is lower than the mutation rate.” As is often true, reality seems to lie somewhere in the middle of these two viewpoints, but the field is still rapidly evolving, with new technology expanding the extent to which scientists are able to re-create history.

Sources:

Nei, M. (2005). Selectionism and Neutralism in Molecular Evolution. Molecular Biology and Evolution,22(12), 2318-2342. doi:10.1093/molbev/msi242

Piertney, S. B., & Oliver, M. K. (2005). The evolutionary ecology of the major histocompatibility complex. Heredity,96(1), 7-21. doi:10.1038/sj.hdy.6800724

Choosing your significant other based on looks is kind of shallow, try smelling them instead!

While discussing the effects of inbreeding on heterozygosity in class, the study of MHC (major histocompatibility complex) dependent mate preference was brought up. The methods, which consisted of men wearing the same shirt two days in a row and women ranking them based on intensity and pleasantness/'sexiness' of smell, seemed unusual and creative to me, so I decided to look it up.

Wedekind, Claus, Thomas Seebeck, Florence Bettens, and Alexander J. Paepke. "MHC-dependent Mate Preferences in Humans." Proceedings of the Royal Society of London. Series B: Biological Sciences260, no. 1359 (June 22, 1995): 245-49. doi:10.1098/rspb.1995.0087.

Some interesting things I learned

• to prepare for the study, female participants were urged to read Das Parfum, a novel that explores the relationship between smell and emotion in order to make them more aware of their sense of smell
• women not taking birth control found the odor of men with dissimilar human leukocyte antigens (HLA) from their own to be more attractive, while women on the pill were more attracted to the smell of men with similar MHC
• women found the intensity and pleasantness of the odor of men with dissimilar MHC to have a negative correlation  
• odors of MHC dissimilar men reminded women of past sexual partners 
• reproduction by couples with similar MHC results in more frequent spontaneous abortion 

Lyme disease

During class Lyme disease was mentioned as an example of a spirochete-shaped bacterial disease, (if I remember correctly). The name “Lyme disease” for some reason sparked familiarity to me at the at moment. I didn’t know why at the time, but after going back and speaking with my mother on the phone, I realized that it was because my grandfather recently had Lyme disease. He lives in the countryside of Wisconsin and was bitten by a tick. This made me want to look more into Lyme disease in general. The symptoms, causes, prevention tactics, but also any experiments/ revelations/ newer information regarding the disease. I began with a google search to identify the basic information about Lyme disease. 

Citation: 

“Lyme Disease.” Mayo Clinic, Mayo Foundation for Medical Education and Research, 5 Dec. 2018, www.mayoclinic.org/diseases-conditions/lyme-disease/symptoms-causes/syc-20374651.

Notes:

***Lyme Disease= an inflammatory disease cause by a bacteria that is transmitted by ticks. 

·     United states: Borrelia burgdorferi and Borrelia Mayonii

·     Europe/Asia: Borrelia Afezelii and Borrelia Garinii

o  àthe 4 types of bacteria that can make Lyme disease

SYMPTOMS

·     Early

o  3-30 daysàbull’s eye pattern rash. It expands slowly over days and can spread to 12 inches across. Typically, not itchy/painful but might be warm to the touch. 

o  Fever, chills, fatigue, body/headaches, neck stiffness and swollen lymph nodes. 

·     Later if untreated

o  Joint pain/swelling (especially for the knees) 

o  Inflammation of the membranes surrounding the brain (affecting memory)

o  Temporary paralysis of one side of the face

o  Numbness/weakness of limbs (impaired muscle movement) 

**Lyme disease= caused mainly by black-legged or deer ticks. Young brown ticks can be smaller than a poppy seed, which can make tick bites incredibly hard to spot. The tick bit however must be attached for 36-48 hours before one can contract the disease. Removing the tick ASAP after noticing is the best way to prevent Lyme disease. 

RISK FACTORS

·     Spending time in heavily wooded areas 

·     Exposed skin (never let pets wander in tall grasses) 

·     Not removing ticks/ properly removing them

PREVENTION

·     Cover up

·     Insect repellent

·     Tick-proof your yard (mow lawn)

·     Always check for ticks

·     Not immune!! (you can get Lyme disease more than once)

·     Remove ticks with tweezers!! After removing a tick put it in alcohol or flush it down the toilet to ensure that it cannot come back and re-attach itself to you!! 

Next, I went on to the UCSB library website and searched the phrase “Lyme disease + new” under “articles”. I came cross a scientific paper regarding a New Approach to a Lyme Disease vaccine. 

Citation: Livey, et al. “New Approach to a Lyme Disease Vaccine.” OUP Academic, Oxford University Press, 1 Feb. 2011, <academic.oup.com/cid/article/52/supp/_3/s266/444992>.

Notes: 

·     Aim of current study= to develop a novel OspA lipoprotein that is stable, safe, immunogenic, and able to generate antibodiesà(a vaccine for Lyme disease that can be distributed to a larger group of individuals)

·     METHODS: 

o  Complimentary overlapping synthetic oligonucleotides were used to generate DNA fragments that were then ligated together and cloned into “Vector pET3oa”

***oligonucleotides= a polynucleotide whose molecules contain a relatively small number of nucleotides

***nucleotides= the basic structural unit of nucleic acids such as DNA. 

***ligate= tie up or otherwise close off (an artery or vessel?)

·     Animal testingà

o  Mice are given tester prevention Lyme disease vaccine

o  Some mice injected with disease

o  Some mice given 8 ticks each (allowing them to feed for up to 5 days)

o  Where possible the infected organism was cultured and the OspA sequence/deduced amino acid was determined for OspA resides 38-262??

·     RESULTS: 

o  All of the mice immunized with low doses of 2 diff experimental vaccines = developed by ELISA (table name?)

o  If I understand the conclusion correctly, they were saying that the experimental preventative vaccines worked to create antibodies for the predicted, specific stand or type of Lyme disease that they were looking at. 

o  Human preventative vaccines for Lyme disease= currently not available

o  Experiment worked for miceàshowed it should be possible to experiment on humans? 

Hoped you all found this as interesting and helpful as I did!